Alignments for a candidate for paaJ2 in Lacinutrix algicola AKS293

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaJ2 in Lacinutrix algicola AKS293

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_055435026.1 ASC41_RS02340 3-oxoadipyl-CoA thiolase

Query= SwissProt::P0C7L2
         (401 letters)



>NCBI__GCF_001418085.1:WP_055435026.1
          Length = 404

 Score =  462 bits (1190), Expect = e-135
 Identities = 234/402 (58%), Positives = 299/402 (74%), Gaps = 1/402 (0%)

Query: 1   MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60
           M+EA+I DGIRTPIG Y G LS+VR DDL A+ + E++ RNP +  E  DDVI+GCANQA
Sbjct: 1   MKEAYIIDGIRTPIGNYKGTLSAVRTDDLGALVISEIVKRNPSIPKEAYDDVIMGCANQA 60

Query: 61  GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120
           GEDNRNVARM++LLAGLP +V G T+NRLC SGL A+  A RAIKAGDGD+ I+GGVE+M
Sbjct: 61  GEDNRNVARMSSLLAGLPFTVPGETVNRLCSSGLSAIIHANRAIKAGDGDVFISGGVENM 120

Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRED 180
           +R P+VM K ++AF   ++M+D+T GWRF+NP M   +GTD M  TAEN+ E   ISRED
Sbjct: 121 TRGPYVMAKPSTAFGGDSKMYDSTFGWRFINPKMQALYGTDGMGNTAENLVEKYNISRED 180

Query: 181 QDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKA 240
           QD FAL SQQ+  KAQ SG LA+EIV V +  +K    +   DE ++P ++LE L  L+A
Sbjct: 181 QDKFALWSQQKATKAQESGRLAKEIVTVEIPQRKKDPIQFSKDEFIKPTSSLEVLGKLRA 240

Query: 241 PF-RANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGP 299
            F +  G +TAGN+SG+NDGAAA IIAS        L P ARIV+ A  GVEPR+MG+GP
Sbjct: 241 AFKKEGGSVTAGNSSGLNDGAAATIIASADAVKKYNLKPLARIVSSAVVGVEPRIMGIGP 300

Query: 300 VPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPL 359
           V A+ + L +AGL++ D+D+IELNEAFAAQAL  +R  G+ D+ P +NPNGGAIA+GHPL
Sbjct: 301 VQASNKALAKAGLTMDDIDIIELNEAFAAQALACIRAWGIADNDPRINPNGGAIAIGHPL 360

Query: 360 GMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           G++GAR+A +A+ EL  +N +YAL TMCIGVGQG A I+E V
Sbjct: 361 GVTGARVAHSAALELQNQNKKYALITMCIGVGQGYAAIIENV 402


Lambda     K      H
   0.319    0.135    0.384 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 446
Number of extensions: 11
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 401
Length of database: 404
Length adjustment: 31
Effective length of query: 370
Effective length of database: 373
Effective search space:   138010
Effective search space used:   138010
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_055435026.1 ASC41_RS02340 (3-oxoadipyl-CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02430.hmm
# target sequence database:        /tmp/gapView.2901609.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02430  [M=400]
Accession:   TIGR02430
Description: pcaF: 3-oxoadipyl-CoA thiolase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-185  602.2   3.2   2.8e-185  602.0   3.2    1.0  1  NCBI__GCF_001418085.1:WP_055435026.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001418085.1:WP_055435026.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  602.0   3.2  2.8e-185  2.8e-185       1     400 []       2     402 ..       2     402 .. 0.99

  Alignments for each domain:
  == domain 1  score: 602.0 bits;  conditional E-value: 2.8e-185
                             TIGR02430   1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaall 73 
                                           ke+yi+d+irtpiG y G+ls+vr+ddl+a+ + ++++rnps+  +a ddvi+GcanqaGednrnvarm+ ll
  NCBI__GCF_001418085.1:WP_055435026.1   2 KEAYIIDGIRTPIGNYKGTLSAVRTDDLGALVISEIVKRNPSIPKEAYDDVIMGCANQAGEDNRNVARMSSLL 74 
                                           69*********************************************************************** PP

                             TIGR02430  74 aGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGw 146
                                           aGlp +vpg tvnrlc+sgl a+  a raikaG+ d+ i+GGve m+r p+v+ k  +af+ + k+ d+t+Gw
  NCBI__GCF_001418085.1:WP_055435026.1  75 AGLPFTVPGETVNRLCSSGLSAIIHANRAIKAGDGDVFISGGVENMTRGPYVMAKPSTAFGGDSKMYDSTFGW 147
                                           ************************************************************************* PP

                             TIGR02430 147 rfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvv 219
                                           rf+npk++alyG+d m++taen+ e++++sredqd+fal sqq++++aq++G +a+eiv+vei+q+k ++  +
  NCBI__GCF_001418085.1:WP_055435026.1 148 RFINPKMQALYGTDGMGNTAENLVEKYNISREDQDKFALWSQQKATKAQESGRLAKEIVTVEIPQRKKDPIQF 220
                                           ************************************************************************* PP

                             TIGR02430 220 dkdehlraettlealaklkavvred.gtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGvep 291
                                           +kde  ++ ++le l kl+a ++++ g+vtaGn+sG+ndGaaa ++as++avk+++l+p ari+++a +Gvep
  NCBI__GCF_001418085.1:WP_055435026.1 221 SKDEFIKPTSSLEVLGKLRAAFKKEgGSVTAGNSSGLNDGAAATIIASADAVKKYNLKPLARIVSSAVVGVEP 293
                                           ********************99865279********************************************* PP

                             TIGR02430 292 rvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGar 364
                                           r+mG+gpv a +k+la+agl+++d+d+ielneafaaqala++r+ g+ad+d r+npnGGaia+GhplG++Gar
  NCBI__GCF_001418085.1:WP_055435026.1 294 RIMGIGPVQASNKALAKAGLTMDDIDIIELNEAFAAQALACIRAWGIADNDPRINPNGGAIAIGHPLGVTGAR 366
                                           ************************************************************************* PP

                             TIGR02430 365 lvltalkqleksggryalatlciGvGqGialvierv 400
                                           ++ +a  +l++++++yal t+ciGvGqG a +ie v
  NCBI__GCF_001418085.1:WP_055435026.1 367 VAHSAALELQNQNKKYALITMCIGVGQGYAAIIENV 402
                                           *********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (404 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 14.18
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources